Stowaway
by altoclefislife
Summary: When a simple mistake causes colossal issues in The Doctor's future, people on the TARDIS start vanishing. But, when assumed coincidences and bad luck become more regular, what will this new team TARDIS do to save themselves and the TARDIS? OC antagonist, brief appearance of the Ninth Doctor and Rose Tyler.
1. Prologue

_Prologue_

 **A/N: New story! I know Martha isn't the most popular companion in the Doctor Who world, but, I think she would be fun to write! The prologue will start when Rose is still with the Doctor (Nine). I've never wrote anything with Nine, so the prologue might be awful. But, we'll see...**

Rose stepped out of the TARDIS with the Doctor following.  
"Oh, wow Doctor! This planet is beautiful. And, it's uninhabited?" Rose asked.  
"Yep. Lucky for you and me! Dalia 3636424 has been uninhabited for three-billion years." The Doctor said.  
"Let's go explore!" Rose said as she pulled on his hand.  
Rose and the Doctor ran around the planet with white grass, purple trees, and a soft purple sky that turned red at night. But the Doctor forgot something...

A shadow saw the open door of the TARDIS and ran towards it.  
The door was closed once the Doctor and Rose returned.

 **A/N: Did you like it? I sure hope so! Tell me if you did!**


	2. Chapter 1

_Chapter_ _one_

 **A/N** : **First** **chapter**! **Let's** **do** **this**! **Oh** , **and** **Ten** **will** **be** **in** **every** **chapter** **from** **here**. **And** **Martha.**

Martha sat on the chair by the console and looked at the corals. She was alone for a bit.

After getting struck by lightning, the Doctor had a bit of a head cold, so he was sleeping it out somewhere, most likely in the library. So, Martha was going through her pockets, and looking up at this strange place.  
The TARDIS hummed as Martha put her feet up on the console. She couldn't help but feel a bit fatigued...  
"Alright then, let's get you home!" The Doctor came in.  
Martha shot up out of the chair in surprise.  
"Well, you got better fast!" Martha said.  
"Time Lord immune system. Gets the sickness in and out in a flash!" The Doctor responded.  
Martha raised her eyebrows. She put her jacket back on and watched the Doctor run around the console. But then, the lights flashed and then went off.  
"Doctor, what happened?" Martha asked.  
"The lights went off." The Doctor ran over to the monitor.  
 _Emergency power activated._  
"What's going on?"  
"I'm not sure. Who's behind you, Martha? Old friend of yours that snuck in?"  
"There's no one behind me."  
"Then explain the shadow."  
Martha turned and saw it.  
The shadow.  
"Let me do a TARDIS life scan..." The Doctor said.  
The search only turned up two life forces. The Doctor and Martha.  
Then why was there another shadow?


	3. Chapter 2

**_Chapter_ _2_**

The Doctor let Martha choose.

"Do you want to stay with me for now or do you want to go home?" This was a side of the Doctor that we don't see often, but in times like this, he needed someone.  
Martha pondered this for a moment. She could be deciding life and death.  
"I want to stay."  
The Doctor nodded. "Good. We might need a medic on our team anyway."  
"Our team? Who else?" Martha asked.  
"I have a old friend that I'd like to meet up with to help us." The Doctor responded.

 ** _Meanwhile_ _at_ _Torchwood_ _three_...**

"Jack, I am going to _kill_ you!"

Gwen Cooper ran around the Torchwood three headquarters, searching every nook and cranny for Captain Jack Harkness.

Jack had run off while Gwen was giving a report on some unusual power outages and even a few deaths. He ran off after hearing a Vworp sound and disappeared from the hub.

"Jack! Where are you?"

 ** _Outside_ _Torchwood_ _three_**

Jack looked at the blue police box that was about thirty feet away from him. He thought he would never see that box again.  
He hadn't seen it since he died. But woke up and then found he couldn't die. Why couldn't he? He would never know.  
He looked at the box like he'd never seen it before.

"Jack!"

Gwen found him and was running towards him. Her target was set and she was almost there.  
But that's when Jack started running. The TARDIS still hadn't done anything since appearing near the base.

"Jack, where are you going?"

"Get back here!"

But he didn't hear her. He just kept running while raindrops shattered on his shoulders.  
When Jack finally reached the TARDIS, he put his hand on the beautiful box. He remembered the Doctor.

 _His_ _short_ _hair_ , _the_ _black_ , _gosh_ , _he_ _liked_ _black_. _And_ _bananas_.

He almost knocked, but instead he just opened the door.

"Ah, Captain Jack Harkness! Just the man I was looking for. Well, for once." The Doctor explained, but whispered for the last bit.  
"Doctor, I've been looking all over time and space for you. And now, I found you." Jack said. "But, you've changed. What happened at the game station?"  
"I saved Rose. She looked into the TARDIS and became the Bad Wolf. I had to suck that energy from her and then I changed." The Doctor responded.  
"Ah. And I understand that she died at Torchwood two?"  
The Doctor's face got very solemn.  
"Yes." The Doctor said in a low, scratchy voice.  
"I'm sorry. But I see you found someone else?"  
Martha smiled, happy that the two men had finally acknowledged her existence.  
"I'm Martha Jones, and you're Captain Jack Harkness?"  
"The one and only." Jack clicked his tounge.  
"Jack, don't, just don't." The Doctor said.

* * *

 ** _Outside_ _of_ _the_ _TARDIS_**

Gwen reached the blue box and looked around it for Jack. She finally decided to go inside the box.  
"Jack, I know you're in here!" Gwen yelled.  
She opened the door and found Jack, some guy wearing a pinstriped suit and had spiky brown hair, and a girl with a red jacket.  
"Oh, hello." The Doctor said.  
"Wow, it's bigger on the inside.. how is that possible?" Gwen said.  
The Doctor simply winked.  
"Doctor, Martha, this is Gwen Cooper. She works for me." Jack said. "Gwen, this is the Doctor and Martha. The Doctor is a old friend of mine."  
Gwen couldn't respond. She really couldn't. The TARDIS was absolutely amazing and she couldn't take her eyes off of it.  
She managed a small "Hi" and a wave. But that was all. But that's when it happened.

 _Whoosh_

The doors closed, the TARDIS shuttered, the lights went out, and the only source of light was the console that was full of energy from the vortex.  
"Doctor, what's going on?" Martha asked urgently.  
The Doctor started working on the console. "Hold on, Jack, open the trapdoor by the console, and Gwen, might get a bit more inside if possible." The Doctor grabbed a box full of wires and a few tools from other planets.  
Jack ran over to the trapdoor and heaved it opened. The Doctor got into the compartment and set to work, shouting orders at Jack to give him a tool or something from the box.  
"I need the reference cord, Jack."  
"What color?"  
"The...um...blue one?"  
"There's not a blue one."  
"Red?"  
"Nope."  
"Green?"  
"That's the only one."  
"Just give me the cord."  
Jack gave the Doctor the green cord. The Doctor was on a mission to save his TARDIS, since whatever shut the lights off, could easily shut down the systems. And kill the TARDIS.  
"Doctor, what are you doing?" Gwen asked. She got a little closer to the trapdoor.  
"I'm creating a generator using extra-temperature controlled glue, to create a system that will withstand the sun storms of Eli's Elite."  
"Okay then. Is there anything I can do?" Gwen asked.  
"You can... get acquainted with Martha. Get to know the team."  
Gwen shrugged. At least it was something.  
"Oh, and until I can get this working, nothing will work, so I need candles. I think I have some under the console. Matches too. They should be there. But if you can't find them, Martha knows." The Doctor said.  
"Okay. I'll get on that." Gwen responded.  
Gwen walked off and went digging for candles and matches. Meanwhile, Jack tried to get reacquainted with the Doctor.  
"So?" Jack said, giving the Doctor a nail.  
"So?" The Doctor responded.  
Jack's voice got lower. "Did you tell her?"  
"No."  
"No?"  
"Nope."  
"I bet you didn't even try."  
"I did!"  
"I doubt you did."  
"I did!"  
"Did you even try?"  
"Yes."  
"Jack, please stop."  
"But, Rose.. I want to know!"  
"I bet you will find out." The Doctor's voice sounded near to tears.  
"Okay, I'm done. See?"  
"Good. Now then, I need the glue."  
"Here."  
Jack watched as his friend's hand appear out of the mechanisms that were below their feet. Jack dropped the glue tube in the Doctor's hand and watched it disappear back into the sea of wires.  
The TARDIS was silent, until Gwen found the candles and matches. Martha grabbed a few from the box that was painted red, but the paint was chipping off due to age. A box of matches was taken from the box and Gwen lit one. She lit one candle as Martha found some paper plates to set the candles on so they didn't get wax everywhere.  
"Gwen? Martha? Did you find the candles?" The Doctor asked.  
"Yes. And the matches, too." Martha responded.  
"Good, now put them, well, everywhere you can until you run out." The Doctor said.  
The girls started placing candles on plates and putting them all over the console room. This went on for about four hours...

"Doc, c'mon. You've been down there for hours. You need to get out of there and rest for a bit." Jack reasoned with his friend.  
"Jack, but I need to..."  
"Come on out."  
"But..."  
"Come out and do something else for a bit. Just rest."  
"Fine. I'm coming."  
Jack helped the Doctor come out from below the floor. Once out, the Doctor laid down on his back and stared at the ceiling. Martha yawned.  
"What time is it? Earth time?" Martha asked.  
"About ten-ish. Jack, do you have a watch?" The Doctor responded.  
"Yes. And you're right. Ten-ish." Jack responded.  
"We'd better get some sleep then." Gwen said. "Who knows what we'll be facing tomorrow."  
"Yeah. But where are we supposed to sleep?" Martha asked.  
"I'll show you." The Doctor said as he got to his feet.  
He led them down a hallway after Jack found his old room.  
"These are the bedrooms. Choose whichever one you'd like." The Doctor said as he walked off.  
"Where are you going?" Martha asked.  
"Same place you are." The Doctor responded.  
"What?" Gwen asked.  
"Doesn't matter." The Doctor responded.  
They all went their separate ways and went to sleep.

 _I'm_ _coming_ _for_ _you_ , _Doctor_."


	4. Chapter 3

_**Chapter 3**_

At two'o clock A.M sharp, the Doctor woke up. He looked around the white bedroom before getting up and ready for the day.  
After getting ready, he went to the console room and got into the compartment. He got the old red box and continued working on the generator.

At about seven A.M, Jack woke up and found his way to the console room.  
"Hey, Doc. Got any coffee?" Jack yawned.  
"I normally would, but if you haven't noticed, he don't have power." The Doctor responded.  
"Oh, right. Sorry Doc."  
Jack sat on the chairs by the console and ended up falling asleep.  
"HA!" The Doctor explained.  
The lights turned on and the TARDIS started humming.  
"Finally! I got it!"  
"Did you get it, Doc?"  
The Doctor looked at Jack with a 'are you kidding me' look on his face.  
"Just messing with you, Doc." Jack said playfully.  
"Don't call me "Doc." Just help me out."  
Jack sauntered over to the door and helped the Time Lord out.  
"Okay, now that we have power, let's do another life scan." The Doctor said.  
The Doctor and Jack walked to the console and the Doctor started a scan. A few minutes later, the scan was complete.  
"I don't get it, I've done two life scans and the only life on here is me, you, Gwen and Martha. But if whatever's causing all the trouble isn't showing up on life scans, then, oh. I think we have a Shadow warrior among us." The Doctor said.  
"A Shadow warrior? Those shadows that have been appearing before... I just cracked a case that Torchwood's been investigating. Thanks Doc!" Jack responded.  
"Well, I think one's in the TARDIS. But how did it get in here?" The Doctor said.  
"Can't they float through walls?" Jack asked.  
"No. They're corporeal, like humans. But they're invisible. They also, apparently don't appear on life scans. But they only exist on one planet that I brought Rose to in my ninth regeneration and I had the door closed and locked." The Doctor said.  
"Are you sure, Doc? What if when the Warrior entered the TARDIS, it closed the door?"  
"I guess that's possible. But what if..."  
A scream emitted from Gwen's room and both men were soon dashing to the source.  
The Doctor burst into the room. "What happened?"  
"Did you see the Shadow warrior?" Jack asked.  
"No." Gwen sniffed. "I-I just had a night terror."  
"Oh, yeah. Um, Shadow warriors can also cause night terrors." The Doctor said.  
"Did you get the power back on?" Gwen asked.  
"Yep. The generator's up and running." The Doctor responded.  
"What time is it?"  
"Seven-fifty nine."  
"Thanks, Jack."  
Jack winked and left the room, leaving Gwen and the Doctor.  
"I-I should get up." Gwen said.  
"Of course. After you're done, come and find me and I'll show you where the kitchen is." The Doctor said as he left, closing the door.

 _Thirty_ _minutes_ _later._...

Jack and the Doctor were trapped.

The Shadow warrior had tried to enter the library and in the spur of the moment, the TARDIS made the door dissapear, leaving Jack and the Doctor stuck in the library to protect her thief and his friend.

"What happened to the door?" Jack asked.  
"The TARDIS took it to protect us." The Doctor responded.  
"Will it come back?" Jack asked.  
"Maybe..." The Doctor said.  
Jack sighed and plopped onto the couch. The Doctor started pacing in a attempt to come up with something. Suddenly, Jack's stomach growled. The Doctor looked at him.

"Hungry?" The Doctor asked.  
"Yeah. Haven't eaten since last night." Jack responded.  
The Doctor snorted. _Puny humans_.  
"Do you have anything to eat?" Jack asked.  
"Let's see..."

After two hours of searching the Doctor's bigger-on-the-inside pockets, the search only turned up some powdered peanut butter that only had about one serving left in it. Jack groaned. But as he groaned, the TARDIS materialized a tray of food for them.  
The tray had a full English breakfast on it and Jack raced over to it.  
"Want any, Doc?" Jack asked as he started stuffing his mouth.  
"No. Not now." The Doctor responded.  
"Your loss."  
The Doctor sat down on the couch and watched Jack devour the food. The Doctor then remembered a book that had been put in every TARDIS since the incident. He walked over to a bookshelf, then flipped the book open.  
"Find something to help us?" Jack asked.  
The Doctor nodded. "This should help us get the door back."

 _Twenty_ _minutes_ _later._...

The Doctor started sonicing where the door was supposed to be in a attempt to create a doorway that would last for about thirty seconds. So far, nothing and the Doctor had been working the doorway for Twenty minutes.  
"Doc," Jack began. "This isn't working."  
"It should. It's in the book." The Doctor responded.  
Jack just shrugged. He didn't have any witty comebacks.

 _Whoosh_

"Doctor, what was that?" Jack asked.

"The Shadow warrior. It found it's way in."


	5. Chapter 4

_Chapter_ _4_

 **A/N** : **Disclaimer** : **I** **don't** **own** **Doctor** **Who** **or** **Torchwood**. **But** **I** **do** **own** **a** **impressive** **comic** **book** **collection**! **Including** **a** **Torchwood** **comic**!

"Where are they?" Martha questioned.  
"I don't know. Last I saw the Doctor and Jack they were... helping me and the Doctor told me to find him to help me find the kitchen." Gwen said.  
"Well, knowing the Doctor, he's probably in the library." Martha said.  
"And knowing Jack," Gwen began. "He's, um, does the TARDIS have a alien artifacts room?"  
Both started laughing. But it slowed when something grabbed onto Gwen's jacket.

"Gwen!" Martha explained as she started chasing after her.  
"Martha, what's going on? Who's dragging me?" Gwen asked.

Gwen vanished behind a corner and Martha chased her.  
Gwen struggled in the creature's grasp. She tried to hit the figure but Martha came around the corner and tripped on Gwen's legs.  
"Martha, I'll be fine, leave me! Protect yourself."  
Gwen pleaded.  
"But I can't. Jack and the Doctor would kill me." Martha said.  
"I'll see you again. Go on!"  
And with that, Gwen Cooper was dragged around another corner, only to be seen by the Warriors.

behind a corner and Martha chased her.  
Gwen struggled in the creature's grasp. She tried to hit the figure but Martha came around the corner and tripped on Gwen's legs.  
"Martha, I'll be fine, leave me! Protect yourself."  
Gwen pleaded.  
"But I can't. Jack and the Doctor would kill me." Martha said.  
"I'll see you again. Go on!"  
And with that, Gwen Cooper was dragged around another corner, only to be seen by the Warrior.


	6. Chapter 5

_**Chapter 5**_

"What are you trying to tell me?"

Jack looked at his friend, the Doctor, who was currently on the floor, trying to find something in a bookshelf.  
"I just told you. The Shadow warrior somehow got in here and now, we need to get out." The Doctor explained, with a annoyed tone in his voice.  
"Yeah... but, Doc? How are we gonna get out?" Jack asked.  
"I'm trying to find a vent. I doubt either of us will fit, but I might be able to get a message to the girls, telling them that we are stuck in the library."  
"Okay. Um, but then how are we gonna get out?"  
"I don't know."  
"I thought you always had a plan!"  
"Well, the plan was to find the vent and contact the girls."  
"The next part?"  
"I'll think of something. AHA!"  
"Did you find it, Doc?" Jack said as he ran over to the Doctor.  
"I found a updating map of the TARDIS." The Doctor pulled a yellowed scroll out and showed Jack the map. "It updates when the TARDIS adds another room. It shows exits and commonly visited rooms."  
"So, we use this to find alternative exits?"  
The Doctor nodded. "Yes. Now, let's find the library."  
He found the library and looked at the outline that marked where a new room began. He found a new door that had a time limit on it.  
"Why does it have a time limit on it?" Jack asked.  
"Because it's going to dematerialize in that time frame. We have to find it and leave the library before the Shadow Warrior finds us again. Allons-y!" The Doctor said.  
They ran and found the door with little time to spare. Jack threw it open and ran inside. The Doctor followed and closed it just in the nick of time.  
"That was a close one. Where are we now, Doc?" Jack questioned.  
"Either a very dark console room, or a back closet." The Doctor responded.  
Jack hit his head on a shelf. "Ow."  
"Closet it is, then." The Doctor said.  
"Is there a light switch?" Jack questioned.  
"Hold on, I'll use the sonic as a torch." The Doctor turned it on.  
A blue light emitted from the silvery contraption, casting a strange and very unnerving glow on the two men.  
"No switch." The Doctor said.  
"Great." Jack started. "We're stuck in a dark closet without a door, without access to food or water, and I bet Gwen and Martha are worried sick about us."  
"Jack, we'll get out if this. We always do. Now, I bet Gwen and Martha are looking for us, but they know how to take care of themselves. They're fine." The Doctor reasoned.  
"You're right. They can take care of themselves and as long as they stick together, the can conquer the world." Jack responded.

 **A/N: I hope you read chapter four...**


	7. Chapter 6

_**Chapter 6**_

"Gwen!"

Martha had just witnessed Gwen Cooper be dragged across the TARDIS and around a corner by a Shadow Warrior. She hadn't moved since the careless dragging of her new friend. She had stood there, looking worn out and out of breath.  
"Gwen!" She tried again.  
Martha fainted.

 _In a dark dungeon like room..._

Gwen was thrown in a dark, jail like cell. She sat up as the door closed. A figure started forming out of thin air.  
"Who are you?" Gwen said.  
"I am Ahtahkakoop, troop of the Shadow warrior tribe. I am on a mission."  
"To do what?" Gwen asked.  
Ahtahkakoop laughed. "Silly girl, why would I tell you my plan?"  
He walked out of the room, but dropped a feather. Gwen reached through the bars of the cage and managed to grab it.  
Gwen looked at the feather and put it in her pocket. The red-and-white feather slid in her coat pocket with ease.  
She looked around in the pitch black cell. She remembered that she had a flashlight in her jeans pocket. She found a small, black flashlight and turned it on.  
A eerie silence fell over Gwen as she walked around her cell.  
 _Crash._  
Gwen turned around to find the origin of the sound. She shined her flashlight around, but didn't find anything that could've caused the crash.  
 _Thump._  
Gwen fell to the floor.

 **A/N: I got the name "Ahtahkakoop" from a site called, "Behind the Name." A friend of mine introduced it to me. The site gives name meanings and languages. "Ahtahkakoop" means "Star blanket" in Cree. It was the name of a early nineteen century chief. I might start using this site more in my stories, and I'll put the name meaning on a author's note. See y'all next chapter, Whovians!**


	8. Chapter 7

_**Chapter seven**_

Martha woke up on the floor of a TARDIS hallway.  
She sat up and looked around. The TARDIS hummed and glowed, and seemed to be attempting to tell Martha something.  
The TARDIS glowed on one particular spot on the wall. Martha walked over and touched it.  
"Martha!"  
A door appeared and The Doctor and Jack walked out.  
"Doctor, Jack! Where were you?" Martha asked.  
"We were trapped in the library, then the Shadow warrior got into the library that had no door, so then we found a closet without a door, and here we are!" The Doctor explained.  
"Gwen. Where's Gwen?" Jack questioned.  
Silence fell over Martha. She looked at the Doctor, hoping he knew something. He shrugged his shoulders and looked at Jack.  
"Where is she?"  
"She...She kinda had a run-in with a Shadow warrior. She got dragged off and taken somewhere. I'm not sure where, though." Martha responded.  
Jack's face went red. "Doctor, does that map give locations of people?"  
The Doctor looked at the map. "Depends. If they've been in the TARDIS for more than three days, then they are considered a passenger. Gwen had only been on the TARDIS for about twenty-four."  
"So we'll have to wait." Martha said.  
"Let the waiting game begin." Jack said.


	9. Chapter 8

_**Chapter Eight**_

 _"Gwen Cooper..."_

 _"What do you want?"_

 _"You... and Jack..."_

 _"Jack and I?"_

 _"Yes..."_

* * *

"You can't have Jack and I! I won't let you!" Gwen yelled as she woke up.  
"Oh, it was just a dream." Gwen sat up and looked around.  
"But the cell wasn't just a dream." Gwen whispered.  
Gwen looked around the grimy cell.  
 _"I've got to get out of here."_ Gwen thought.


	10. Chapter 9

_**Chapter nine**_

"Has it been three days yet?" Jack asked.  
"No. It hasn't even been her second day on the TARDIS." The Doctor responded.  
Jack groaned. The Doctor looked at the map.  
"Oh!" The Doctor yelled suddenly. "I found someone!"  
"Is it Gwen?" Martha asked.  
"No." The Doctor responded.  
"Then who is it? There's only four of us on here. You, me, Martha, and Gwen." Jack reasoned.  
"I think we just found the Shadow warrior." The Doctor said.


	11. Chapter 10

_**Chapter 10**_

"What!?" Martha and Jack said simultaneously.  
"Or Shadow warriors." The Doctor said.  
"Plural? Really." Martha said.  
"Another reason to find Gwen." Jack said.  
The Doctor rolled the map up. "Just about fifteen hours until Gwen will appear on the map. Then we should be able to find Gwen."  
"Isn't there a way that you can somehow hack into the map and get Gwen's name on it?" Jack asked.  
"I don't know. I'll have to test it." The Doctor responded.  
"Then let's test it. We have to find Gwen, then stop the Shadow warrior." Martha said.  
"You mean, Shadow warriors." The Doctor said.  
"No, there's only one, right?" Jack questioned.  
"Looks like our shadow warrior had a friend." The Doctor said.


	12. Chapter 11

_**Chapter 11**_

Gwen was mulling her options as she looked around her dark cell. She yelled out for Jack, the Doctor and Martha day after day. But today, she cried out for Ahtahkakoop.

"Yes, my sweet?" The Shadow Warrior said as he appeared in front of Gwen.

"Don't call me your sweet if you want me to comply with the plan." Gwen rasped.

Ahtahkakoop looked at her.

Gwen had finally come around.


	13. Chapter 12

_**Chapter twelve**_

The Doctor was trying every setting on his sonic screwdriver, other than the fire setting. Seriously, who sets a magical map on fire?

Jack kept making faces and looking over the Doctor's shoulder. Martha kept pulling him away from him so he could proceed with the map.

"So, have you found Gwen yet?" Jack questioned.

"No, but I'm almost out of settings. There's not much else we can do." The Doctor said as he put the sonic screwdriver back in his pocket.

The monitor lit up.

"The only thing we can do is wait." The Doctor said, turning to Jack and Martha.

The screen turned to static.

"But, the TARDIS is infinite. She's in here somewhere." Martha reasoned.

The screen started to come into focus.

"However, that's too much ground to search. We need to find Gwen soon so we can get back to banishing the Shadow Warriors."

The screen showed Gwen and Ahtahkakoop, standing side-by-side, cackling madly.

"Doc, what is that?" Jack questioned.

They all turned around to look at the monitor and saw Gwen and Ahtahkakoop.

"Gwen? Where are you? Are you okay?" Jack ran towards the monitor.

"I'm good. I'm great. But you need to give us what we want." Gwen said.

"Gwen, what's wrong? Who's behind you?" The Doctor walked over to Jack.

"I am Ahtahkakoop, guard of the Shadow Warriors. Cooper is on my side now. You will give us the last Time Lord and the last Time And Relative Dimensions in Space. We want control of Torchwood three." Ahtahkakoop said.

"No. I won't let you have them." The Doctor and Jack said simultaneously.

"Okay then. You have six hours. You heard our demands and you shall comply with them." Ahtahkakoop disappeared.

The screen went black.

"Why didn't he try to negotiate?" Jack questioned.

"I'm not sure. Normally, Shadow Warriors are fantastic negotiators. Once I gave a Cybermen's hand for a ear of corn." The Doctor said.

"Eh. Probably the same value." Jack said.

An uneasy laugh spread across the TARDIS as Jack and the Doctor walked over to Martha.

"What should we do?" Martha asked.

"There's not much we can do. By the time the map gets Gwen's location, we would have to give in to his demands." The Doctor said.

"Wait, so we're going to give in?" Martha asked.

"We don't kn-" Jack started.

"DOCTOR!"

"MARTHA!"

Martha was being pulled away out of the room by a Shadow warrior.

"Jack, follow her!" The Doctor said as he started running.

Jack and the Doctor followed the Shadow warrior. Or at least, they tried to.

They both got knocked over by a Shadow warrior as they ran after Martha.

Martha screamed and looked at the Doctor as if he was her only hope for escape. Martha kicked and screamed like a toddler being pulled away from their favorite toy store.

Then, she made contact.

The Shadow warrior dropped her as if she'd burned him. Martha made a run for it. She had to get out of the hallway.

Jack and The Doctor both were up now, running back to the console room. They never realized Martha had escaped.

Martha was almost to the console room when she stopped. She thought of something.

Then, she ran towards the location of the Shadow Warriors.


	14. Chapter 13

_**Chapter thirteen**_

Martha had a plan. A good one, if it worked.

She had decided to become a double agent after she had freed herself from the Shadow Warrior.

She, first off, had to locate the Shadow Warrior's hideout. Or a old, grimy dungeon.

She found both.

Martha crept around a corner and noticed Gwen's dark, black hair.

Time to eavesdrop.

Martha hid behind the corner and prepared herself for what they were about to discuss.

"We can take control of the TARDIS if we take down the team. But, the Doctor and Jack will be harder." Gwen said.

"Why? Are they immortal? Will they be hard to capture?" Ahtahkakoop questioned.

"Jack can't die. I don't know about the Doctor." Gwen said.

Ahtahkakoop turned. "Why do you not know about the Doctor?"

"I only just met him." Gwen started. "I don't know much about him."

"Then, find out. We know he is a Time Lord, however, we do not know what is special about him."

Gwen nodded.

"I will transfer some of my invisibly essence to you for a hour use. Go to the library and find something on Time Lords. He must have something of his kind in the library or, maybe a room."

Gwen looked at him. "How will you do it?"

"Hold out your arm." Ahtahkakoop said.

Gwen held her arm out, and Ahtahkakoop put his hands on her long jacket sleeve and pushed it back behind her elbow. He then closed his eyes and orange energy streamed out of the hand and into Gwen's arm.

Gwen winced. Her face scrunched in pain. Then, she screamed.

Martha ran.


	15. Chapter 14

_**Chapter Fourteen**_

 _ **A/N: And, I forgot to upload yesterday. Sorry about that! I'll upload another chapter tonight since I forgot yesterday...**_

"Well, now we need to somehow get both Gwen and Martha back." Jack said.

The Doctor looked at him. "Yes, I know." He said.

"Doctor, Jack, I found Gwen!" Martha panted as she ran into the room.

The Doctor looked at Martha. "How did you-"

"I fought him off. But, I found Gwen." Martha responded.

"Where is she?" Jack questioned.

"A dungeon room. But she's going to the library to find out more about the Doctor. " Martha answered.

"How did you find this out?" The Doctor asked.  
"I found the hideout. I have a plan that might work well for us."

Martha suggested the plan to the Doctor and Jack.

"Spy? It's a good idea to work with..." Jack said.

"Martha," the Doctor said. "Just be careful."

"I will Doctor, I will."


	16. Chapter 15

_**Chapter 15**_

Gwen ran through the library, grabbing books, looking through them, and jotting stuff down.

The door was back now, thanks to Ahtahkakoop and his Shadow Warrior army.

Gwen looked up at the ceiling. Then, she turned...

"Hello, Gwen."

Gwen jumped and dropped the book she was holding. "Martha!"

Martha walked up to Gwen. "You have a appointment."

"With who?" Gwen questioned.

"The Doctor." Martha answered.

"Martha, get down!" Jack stood behind Martha with a tranquilizer.

The dart landed on Gwen's shoulder, and she fell to the floor.

"You grab her legs and I'll grab her arms." Jack said as he picked Gwen's arms off the ground.

Martha picked Gwen's legs up, and they started walking to the med bay.


	17. Chapter 16

_**Chapter 16**_

The Doctor was ready.

All the preparations for Gwen's scan. The Doctor knew that something was wrong with Gwen. He could sense it.

He was just waiting for Jack and Martha.

He ran across the room and looked down the hall. Just a few minutes, hopefully.

He checked the scan to see if everything was ready.

Everything was ready to go. He just needed Gwen.

 **Meanwhile...**

Jack and Martha carried Gwen through the TARDIS corridors.

"The Doctor has the med bay set up to figure out what's wrong with Gwen. Hopefully it's nothing serious." Martha said.

"Good." Jack said.

Martha looked at Jack. "Are you okay?"

Jack looked around. "Yeah. I'm just worried about Gwen."

"Jack, we'll get her back on our side." Martha said.

"We're here." Jack said as Martha walked into the med bay.

The Doctor looked up from something he was doing. "Put Gwen on this bed." He pointed to a white hospital bed in the corner of the room.

Martha and Jack placed Gwen on the bed and the Doctor ran over. The Doctor hooked something up to Gwen and turned to a computer on a desk.

"What's that?" Martha questioned.

"A scanner for any unknown elements that might have been inflicted by the Shadow Warrior." The Doctor said as he typed something in.

"Ahtahkakoop, where are you?" Gwen murmured.

Jack looked at Gwen. "What did she say?"

The Doctor looked at Gwen with worry.

"That's the Shadow Warrior's name."

"What's the significance of that?" Martha questioned.

"Remember the lilith. The power of a name." The Doctor said.

"But would that work?" Martha questioned.

"Maybe. The Shadow Warrior would be transported back to the village it came from." The Doctor said.

"Can we do it with the other warriors?" Jack questioned.

"Yep. And, we still have the map. The names will be difficult to pronounce, but maybe we'll get lucky." The Doctor said.

The scan began.

The Doctor unrolled the map and found Ahtahkakoop's name.

"Found him."


	18. Chapter 17

**Chapter 17**

"I sense something peculiar." Ahtahkakoop said. He pointed to another Shadow Warrior. "Check on Gwen. She is in the library."

The Shadow Warrior nodded and ran off. Ahtahkakoop turned to a map.

"The Doctor and his team seem to always be in the console room, as they call it. So, we will check there. Then we will check here, the library. Then the med bay. We must capture Jack and the Doctor. Grab your stunning arrows. We move."

Ahtahkakoop and his troops were officially at war with team TARDIS.

Meanwhile in the med bay...

"Um, Doc? Ahtahkakoop is on the move with an army of Shadow Warriors." Jack said.

The Doctor looked up from the computer monitor and ran over to the table with the map on it. "He is."

"Where is he going?" Martha questioned as she walked up to the Doctor and Jack.

"It looks like the console room." The Doctor observed.

"They might try to steal the TARDIS. We need to move." Jack said.

Both the Doctor and Martha nodded.

"Martha, stay here and watch Gwen. Jack and I will confront Ahtahkakoop." The Doctor said as he followed Jack.

"Okay. Wait!"

The Doctor and Jack stopped.

"Is there anything specific that I need to do?" Martha questioned.

"Just watch the monitor. Shout if the numbers go down." The Doctor said as he and Jack ran off.

Martha walked over to Gwen and pulled a chair over.

She sat down and eyed the monitor. The current number was eight.

Then, it became seven.

"Doctor!"


	19. Chapter 18

**Chapter 18**

 **A/N: I don't own Doctor Who and Torchwood. If I did, then I'd probably own a island.**

The Doctor looked at his surroundings.

Jack was on the floor, parts of the room were on fire, arrows were stuck in the wall and the Shadow Warriors were gone.

The battle had escalated quickly, with the flaming arrows.

"Doctor!"

The Doctor turned to the source of the voice. He put out one of the flaming arrows and ran to the source of the voice.

"Martha, we got the Shadow Warriors out of the TARDIS. The power of a name." The Doctor said.

"The number went down." Martha said. "What should we do?"

The Doctor ran over to the monitor. "We're losing Gwen. There's something inside of her."

Martha urgently walked over to the Doctor. "What?"

"Ahtahkakoop."


	20. Chapter 19

**Chapter 19**

"How is Ahtahkakoop in Gwen?" Martha questioned.

"He must have transferred invisibility energy into her. With that, he can lock onto the TARDIS and Gwen's gone. Stupid, stupid Doctor!" The Doctor answered.

"What should we do?" Martha questioned.

"We need to suck the energy out of her. Then, Ahtahkakoop can't transport here." The Doctor dug around in a drawer. "Hook this up to the monitor, then stick this in her arm." The Doctor started to run off.

"Where are you going now?"

The Doctor's head appeared in the doorway. "I have to find Jack."

He ran off, and Martha hooked the mechanism, a I.V. looking thing with a computer cord at the end to the monitor, then put the I.V. part on Gwen's arm.

"Doctor, please hurry."

 _ **Meanwhile...**_

The Doctor entered the room where the battle had took place to see Jack trying to figure out what had just occurred.

Jack noticed the Doctor enter the room. "Doc, what did I miss?"

The Doctor swallowed. "A battle."

"How bad of a battle?"

The Doctor walked over to Jack. "Brutal. You got shot by a flaming arrow and died."

"Oh."

The two men stood in silence. Jack broke it. "What happened?"

The Doctor shook his head. "The Shadow Warriors are gone. That's all that matters."

"You don't remember, don't you?"

The Doctor shook his head again. "Nope."

"How's Gwen?" Jack questioned.

The Doctor remembered how he left Martha in the med bay to tend to Gwen. "Martha!"

The Doctor ran off.

"Doctor? Doc? What's wrong?" Jack questioned before he decided to run off.

Back in the med bay...

"Martha!"

Martha looked up at the Doctor. "She's ready for extraction."

The Doctor ran over and typed on the keyboard. "The program is running. Watch Gwen!"

Jack entered the room. "What did I miss?"

Martha shot Jack a look.

"Martha, hold this!" The Doctor said as he tossed a long cord into Martha's arms.

Golden energy swirled around Gwen as the machine extracted some from her body.

Jack turned and noticed Gwen. "Cooper!"

"Jack, we'll save her. Don't worry." Martha said as she ran over to him.

"Torchwood needs her. She replaced Sally." Jack said.

"She'll be okay."

"Martha! I need the cord!" The Doctor said.

Martha tossed the cord to the Doctor and the Doctor plugged it into the wall and hooked a syringe to the end of the cord.

The Doctor ran over to Gwen and put the syringe in Gwen's arm, then pushed the top of the syringe to allow a clear liquid to enter her body.

"The solution should kill most of the remaining energy off." The Doctor explained.

"Rhys... Jack...Martha...Doctor..." Gwen murmured.

"She must be coming to." Jack said.

"Ahtahkakoop, help me. I'm dying."


	21. Chapter 20

**Chapter 20**

"She said his name. Is he coming?" Martha questioned.

The Doctor ran over to the monitor. "Only two percent of the energy remains in her. I don't know what's wrong. "

"She wasn't brainwashed, was she?" Jack questioned.

"No. Wait... aha!" The Doctor exclaimed.

"What?" Martha questioned. "Is all of the energy out of her."

"Yes, and, with that, her memory of the whole experience. She shouldn't remember the Shadow Warriors." The Doctor anwsered.

"Well, let's get back to Cardiff. I think I should stick to catching aliens for now." Jack said.

"Well, I believe the Cardiff portion, but, I think you would still go with me of you had the chance." The Doctor said.

Martha started to take Gwen off of all of the things that were saving her.

"Well, let's go back to the console room and we'll go back Cardiff." The Doctor ran to the console room.

As the Doctor flipped the switches to get the TARDIS going, Jack got Gwen from the med bay and placed her on the captain's chair.

"We're here." The Doctor said as he ran to the doors.

Jack gathered Gwen up in his arms and carried her to the doors.

Once they were outside of the TARDIS, Jack walked out to the area they would enter Torchwood from.

Jack nodded in a goodbye to the Doctor and the Doctor nodded back. And with that, they vanished under the concrete.

Martha ran out of the TARDIS. "Hey, where's Torchwood?"

"It doesn't matter." The Doctor said. "So, where to next?"

Martha laughed. "Oh, I don't know. Where should we go?"

 **A/N: Well, that's the last chapter! I'm working on a "Doomsday" fix-it, "Rewind". This one might take a while, so just know that. Thanks for reading the story and I hope you check out my other stories. I'm not sure if I'll write more _Torchwood._ Maybe once I finish the series. Well, thanks for reading!**


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